There are two ways the clearance can be too small. If the valve head diameter allows it to actually fit within the relief, but the edge of the valve head is too close to the relief, then you can increase the diameter of the relief to create the clearance you need. This may also work if the diameter of the valve is larger than the relief, such that it won't fit into the relief at all.
If the valve fits within the relief, but the relief isn't deep enough to provide enough clearance, then the reliefs must be made deeper. If that's the case, that's pretty difficult to do well with a Dremel tool. If the reliefs have to be deepened, then most folks either have a machine shop cut the pistons, or they use a tool/cutter that's designed to be driven by a drill through the valve guide to cut the relief deeper. I know that Isky sells such a relief cutter - you might be able to find it online.
At some point, however, you'll have to measure to know what you may, or may not, have to do.